I see. Maybe the instruction set for 486 and arm are different. Thats maybe the main problem here right?
The instruction set of UNO/ATmega328 and DUE/SAM3X8E are different; but, the high level commands of Wire.h Library are well executed in both platforms!
So, it is obvious what else to be added with the 30 millions lines of codes of WIN2000 to make it working with DUE.